When Gospel Library (iPad) downloaded new content for v. 2.1, all of my previous highlighting was lost. All I have now are the notes I added to certain verses. And unlike before, the verse with the appended note is highlighted in an ugly yellow.

Furthermore, the new menu to highlight a verse requires extra steps and the color scheme is not the same as previous. The problem with a change like this is for those of us that use colors to track certain gospel themes, the previous highlighting patterns will not match the new ones.

I love the app but this is a very frustrating change, particularly after investing so much to get "my scriptures" looking a certain way or containing personal thoughts and inspirations.

The Known Issues list (you can view this within the app by pressing the Information icon at the top right) includes what you've described about losing annotations. As for the change in colour schemes, etc., I believe that is to bring it into conformity with the highlighting functions on LDS.org. The new version of Gospel Library includes the ability to sync annotations with your LDS.org Study Notebook, so the two systems need to be compatible. I'm not sure if you'll be able to recover the lost highlighting, but because of the new sync feature any marking done in the future will be backed up to your LDS account.